Ever since the terrorist attacks of Sept. 11, 2001, reports have circulated that the U.S. airline security apparatus is targeting political activists for strict scrutiny and special searches, sometimes forcing them to miss flights. Despite the accounts of peace activists, civil liberties lawyers and left-wing journalists, federal agencies wouldn't confirm the policy and airline officials wouldn't discuss it, and so the stories had the feel of urban legend.

But in documents released this week in a federal court case in San Francisco, the U.S. Transportation Security Administration (TSA) confirmed for the first time that it keeps not just a list of potential terrorists barred from the air, but also a list of "selectees" who are subject to strict security checks before they're allowed to board commercial aircraft. The agency has revealed almost nothing else about the selectee list, and is fighting in court to keep secret the names of people who are on it and the standards for putting them there.

It appears, however, that the list may contain thousands of names. Officials at the ACLU of Northern California, which is pressing the Freedom of Information Act case filed by two leftist newspaper editors, says it learned from authorities at Oakland Airport that there is an 88-page typed list of names. Between Sept. 11, 2001, and April 8, 2003, the ACLU says, more than 363 passengers were stopped at San Francisco and Oakland airports, either because their names appeared on that list or because their names were similar to names on a separate "no-fly" list made up of criminals and people with suspected terrorist ties.

Evidence compiled in a series of interviews suggests that activists on the left and right have been affected, as have many Arab Americans. That has civil liberties experts warning that the airport security checks have a chilling effect on routine political activity that is unprecedented in recent times.

"All the secrecy surrounding these lists, and the very fact that the TSA refuses to say how it compiles them, is outrageous," says Barbara Olshansky, an attorney with the left-leaning Center for Constitutional Rights. "It shows that this administration has no respect at all for the Bill of Rights, which guarantees the right of free speech and association and the right to travel freely. They're not balancing security and freedom. They don't care about freedom and civil liberties at all."

Olshansky has firsthand knowledge of the government policy: She says that she's been subjected to strip- and full-body searches every time she's flown since 9/11, even though she has no criminal record. Last November, she told Salon that she had been strip-searched on four flights she'd made on business; this week, she reported that she was specially targeted again for a search in February while trying to board a plane with her husband for a vacation trip to Puerto Rico.

"We had chosen Puerto Rico in part because my husband was afraid of what they'd do to me if we tried to return from a foreign trip," she says. Puerto Rico, a U.S. territory, is a domestic flight that doesn't require going through immigration or customs.

Salon first reported last November that the Transportation Security Administration keeps a list of about 1,000 people who are deemed "threats to aviation" -- many with links to terrorism -- and who are barred from flying under any circumstance. But that didn't seem to explain the unusual security standards applied to political activists and others with no visible link to terrorism or criminal activity. They were generally allowed to board planes after being searched.

A 71-year-old Milwaukee nun and peace activist was stopped from boarding a flight to Washington, where she and a group of students planned to lobby the Wisconsin congressional delegation against U.S. military aid to Colombia. An art dealer who'd been a high-ranking staffer in Ralph Nader's 2000 presidential campaign had been barred from a flight to Germany after telling other passengers in the check-in line that President George W. Bush "is dumb as a rock." And two journalists, Rebecca Gordon and Jan Adams of the antiwar magazine War Times, were told by an airline clerk that the were on "the FBI no-fly list." Even executives at the Eagle Forum, Phyllis Schlafly's old-school conservative group, expressed concern that several of their members had missed flights because they were delayed and questioned at airport security checkpoints.

At the time, a spokesman for the TSA told Salon that in all likelihood, most such passengers were not on the no-fly list for terrorists and criminals. Instead, he hinted, there might be a second list, but he declined to be more specific and the agency officially denied it.

Efforts by the Wall Street Journal to solve the mystery resulted in an April 22 story concluding that most of the problems innocent fliers experienced resulted from computer systems that were "flagging numerous travelers whose names are merely similar to one of those on the [no-fly] list" for terrorists and criminals. For example, the story said, Sister Virgine Lawinger, the Milwaukee nun, had been stopped not because of her politics but because one of the students in her group had the surname of Laden -- a name the TSA flagged apparently because it is shared by a notorious Islamic terrorist.

Certainly that explains some of the stops. In one case, the Journal suggested, retired Coast Guard Cmdr. Larry Musarra has been stopped several times by Alaska Airlines check-in clerks because his name pops up on the list thanks to the M-U-S that begins his name; airline computers apparently flag that as a possible Middle Eastern name. But all too often, people being stopped have anti-establishment protest backgrounds, like Olshansky, whose name doesn't seem to resemble that of any terror suspects, and who has never been offered an explanation for the repeated security delays at check-in.

The Journal article made no reference to a second list.

Gordon and Adams, working with the ACLU, filed suit in federal court in San Francisco. The Transportation Security Administration, established in November 2001 to provide security for the nation's transportation system, acknowledged for the first time earlier this week, in response to a Freedom of Information Act request filed by the ACLU on Gordon's and Adams' behalf, that it has developed and maintains two lists of people that it considers risks to air travel -- the no-fly list, and a list of selectees who are subject to "special security checks" but who can be allowed to board.

On Friday, Gordon and Adams will attempt to learn more when ACLU attorney Jayashri Srikantiah is expected to ask U.S. District Court Judge Charles Breyer to order the TSA and the FBI to produce more detailed information about how the list is compiled and what guidelines and procedures it has in place, and what instruction it gives to airlines when it provides them with the lists for its check-in computers.

Adams, 56, recounted her airport stop in an interview this week with Salon. "We were held by the local police, who said that we weren't under arrest, but were being held until they could check to see if we were on a 'master list,'" she said. "If we were, they said that we'd have to be held until the FBI decided what to do with us. But we apparently weren't on that list, and so they finally let us fly.

"The funny thing," she added, "is that nobody bothered us on our return flight on the same airline. But much later, I had the same thing happen as I was boarding a flight in Chicago. It doesn't make you very confident about the TSA's security operation."

Srikantiah says that to date the TSA has not even confirmed whether the two plaintiffs are on either of its lists. "They have not been very forthcoming with information in response to our FOIA request," she said. But what the agency has said -- and has left unsaid -- worries her.

"We asked them whether people could be placed on the lists for constitutionally protected activities like publishing an anti-government newspaper or participating in protest activities," she said, "and they declined to respond. That is troubling because they should be saying that constitutionally protected activities will not land someone on a watch list."

Liberals aren't the only ones concerned about what the TSA is doing. "It's pretty clear that some lefties have missed their flights just because of things they've said," says Larry Pratt, executive director of the ultraconservative Gun Owners of America organization. "This kind of thing should not be happening to American citizens. I think there's something smelly about the explanations being given by the TSA."

William Olson, a constitutional lawyer in McLean, Va., who specializes in conservative issues and clients, expresses similar concern about the security lists. "Certainly the ability of an American citizen to travel freely is among the most fundamental civil liberties," Olson said. "Lists like this, where no one is accountable for who gets on it, and where there's no way to get off it once you're on, are a bad thing, and bring to mind a police state. You do get the sense these days that the rule of law is crumbling."

Last November, when Salon broke the story that the Transportation Security Administration might have two flight-security lists, a spokesman at the agency explained that it doesn't generate the names, but rather compiles the names from lists provided by other federal law enforcement and intelligence agencies. The spokesman said at that time that the agency itself had no guidelines for putting someone's name on the list, and no procedures for people wrongfully placed on the list to get off.

The ACLU's Srikantiah says that opens the door to abuses. "There should be uniform guidelines for a list like this, and standard procedures for the airlines to follow when someone's name appears on a list," she said. The dangers such lists pose is compounded, she adds, because they are being provided to the airlines, private companies in which employees are not trained in law enforcement.

Even after the administration acknowledged the existence of the two lists, the FBI declined to be specific about what guidelines govern who gets placed on either list. To get onto the no-fly list, said FBI spokesman Jeff Lanza, "someone would have to be linked to terrorism, based upon an FBI investigation.

"Of course, there are other agencies that might input names to that list, and I can't answer for them," Lanza added. "But nobody would be put on that list simply for engaging in constitutionally protected activity or for being arrested at a protest."

For the selectee list, Lanza said, "There are more databases they pull from. Those names wouldn't have to be approved by someone on the terrorism task force. It's slightly broader. But protest activity alone still shouldn't put you on it." At another point, however, Lanza suggested that some activities, such as "chaining yourself to a gate at a military base and blocking traffic" might be different, even if they had no connection with violent or terrorist activity.

Adams isn't so sure, and she wonders whether First Amendment activities alone could get someone blacklisted. "Rebecca and I are two middle-class white ladies," she says. "We don't have arrest records. Our only activity is War Times."

In its response to the ACLU's Freedom of Information action, the TSA declined to say that individuals would not be placed on a selectee list simply for anti-government speech or protest activity. And though the agency has conceded that many names are mistakenly on the list because of glitches in airline computer software and other reasons, it also said it doesn't track how many times air travelers have been incorrectly stopped, saying there is "no pressing need to do so."

Sometimes the stops discovered by the ACLU at Bay Area airports have been humorous, and suggest that the lists could use some refinement and updating. One flier with the unfortunate surname of Padilla was stopped at a Southwest Airlines gate. He was allowed to board after the FBI determined that the Padilla in question -- accused "dirty bomber" Jose Padilla -- was already in custody and being held as an enemy combatant in a military brig in South Carolina. A passenger with the name Hussein was stopped at a Southwest Airlines gate and barred from boarding. After the FBI was called in, he was allowed to fly on.

Efforts over this week to get a response from the Transportation Security Administration went unanswered. A receptionist at the agency advised several times that "everyone is busy."